Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination

Abstract

IMPORTANCEAlthough horseshoe bats are the primary reservoir of SARS-related coronaviruses (SARSr-CoVs), it is still unclear how these bat viruses have evolved to cross the species barrier to infect civets and humans. Most human SARS-CoV epidemic strains contain a signature 29-nucleotide deletion in ORF8, compared to civet SARSr-CoVs, suggesting that ORF8 may be important for interspecies transmission. However, the origin of SARS-CoV ORF8 remains obscure. In particular, SARSr-Rs-BatCoVs from Chinese horseshoe bats (Rhinolophus sinicus) exhibited <40% amino acid identities to human/civet SARS-CoV in the ORF8 protein. We detected diverse alphacoronaviruses and betacoronaviruses among various bat species in Yunnan, China, including two SARSrRf-BatCoVs from greater horseshoe bats that possessed ORF8 proteins with exceptionally high amino acid identities to that of human/civet SARSr-CoVs. We demonstrated recombination events around ORF8 between SARSr-Rf-BatCoVs and SARSr-RsBatCoVs, leading to the generation of civet SARSr-CoVs. Our findings offer insight into the evolutionary origin of SARS-CoV ORF8 protein, which was likely acquired from SARSr-CoVs of greater horseshoe bats through recombination.

Molecular Evolution of Human Coronavirus Genomes

“…Numbers indicate bootstrap support. CoVs are colored according to [14,15]. Analysis of the ORF8 region revealed high sequence identity with civet/human SARS-CoV.…”

“…Analysis of the ORF8 region revealed high sequence identity with civet/human SARS-CoV. Two groups came to the conclusion that recombination within SARSr-Rs-CoVs or between SARSr-Rs-CoVs and SARSr-Rf-CoVs led to the acquisition of an ORF8 closely related to that of civet/human SARS-CoV and ultimately originated the virus responsible for the human epidemic [14,15]. Interestingly, Lau and coworkers also reported that the ORF8 region has a dN/ dS = 3.5 in SARS-CoVs isolated from humans (but not in SARSr-BatCoVs), indicating the action of positive selection (Box 1) [14].…”

“…Two groups came to the conclusion that recombination within SARSr-Rs-CoVs or between SARSr-Rs-CoVs and SARSr-Rf-CoVs led to the acquisition of an ORF8 closely related to that of civet/human SARS-CoV and ultimately originated the virus responsible for the human epidemic [14,15]. Interestingly, Lau and coworkers also reported that the ORF8 region has a dN/ dS = 3.5 in SARS-CoVs isolated from humans (but not in SARSr-BatCoVs), indicating the action of positive selection (Box 1) [14]. This finding is interesting per se and becomes even more important considering that, early in the human epidemic, SARS-CoVs acquired a signature 29nucleotide deletion which split ORF8 into two functional ORFs (ORF8a and b) [16].…”

“…This finding is interesting per se and becomes even more important considering that, early in the human epidemic, SARS-CoVs acquired a signature 29nucleotide deletion which split ORF8 into two functional ORFs (ORF8a and b) [16]. These findings suggest that rapid evolution of ORF8 might facilitate host shifts [14]. This possibility is, however, questioned by the presence of additional SARS-CoV human isolates that carry independent and larger deletions in the ORF8 region [16].…”

“…HCoV-OC43 is thought to have shared a common ancestor with BCoV around 120 years ago [87]. As for SARS-CoV and MERS-CoV, molecular dating studies estimated that they diverged from bat CoVs in the last three decades [14,88]. Finally, the MRCA of HCoV-HKU1 extant lineages was estimated to have existed in the 1950s [60].…”